Writing documents in R Markdown is relatively
straightforward once you know some of the
basics. You can create many different formats, including
.pdf, .html, and .doc, and
customize them in a variety of ways.
There are a number of existing templates available in the rticles
package that you can use for knitting your document to a specific style
in .pdf format. For .html formats, there are a
variety of “themes” available
as well. For example, this document was created with the
spacelab theme.
Task: Open RStudio and from the menu options select File > New File > R Markdown…
Tip: You can change the Title, Author, and Date, fields here, but we’ll do that later.
Task: Leave the Default Output
Format as HTML and click on
OK.
Tip: You now have a new .Rmd file ready
for editing, which includes some placeholder text and code blocks.
Every Markdown document begins with a section of plain text written in YAML (“YAML Ain’t Markup Language”). This block of human readable code is used to define some of the document’s metadata such as the title, author, and date. It is also used to specify the document’s format (eg, HTML or pdf) and its layout (eg, theme, font).
Tip: The front matter is defined in a block of text
that begins and ends with 3 dashes ---.
Here is the YAML for our new simple HTML document:
---
title: "Untitled"
author: "Mark Scheuerell"
date: "10 February 2023"
output: html_document
---
The YAML can include a lot more information as well, including fields for various pre-defined themes, a table of contents, adding citations and formatting references, and whether to use other files as formatting templates. For example, here is the YAML for this document with today’s class notes:
---
title: "Using R Markdown for publications"
subtitle: "Part 1"
date: "10 February 2023"
output:
html_document:
theme: spacelab
highlight: textmate
css: ["lecture_inst.css", "fontawesome.css", "solid.css"]
toc: true
toc_float: true
toc_depth: 3
bibliography: "references.bib"
csl: "ecology.csl"
---
You can write nicely formatted equations in R Markdown using LaTeX language constructs. Although the initial leap into LaTeX can be a bit daunting, it gets much easier with some practice and help from the many guides available online (eg, math and document).
Here are a few things to help you get started (with examples below):
The default typeface is italic, which is commonly used to indicate a scalar; vectors and matrices are typically denoted with bold face, but you’ll need special coding to indicate them as such;
Sub- and superscripts are denoted by _ and
^, respectively; any text/number longer than one
character/digit must be enclosed in curly braces
{}
You can include equations inline by enabling the “inline math mode”
through the use of a single dollar sign ($) at the
beginning and end of the equation. For example,
The errors are normally distributed, such that $e_{i,j} \sim \text{N}(0, \sigma^2)$.
will render as
“The errors are normally distributed, such that \(e_{i,j} \sim \text{N}(0, \sigma^2)\).”
In many cases, you may want to have your equations set apart from the
text on lines by themselves. To do this in Markdown, begin and end the
equation block with 2 dollar signs ($$). If you want
equations on multiple lines, use \\ to indicate a line
break. For example,
$$
y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\
e_{i,j} \sim \text{N}(0, \sigma^2)
$$
will render to
\[ y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\ e_{i,j} \sim \text{N}(0, \sigma^2) \]
and
$$
\mathbf{x}_t = \mathbf{B} \mathbf{x}_{t-1} + \mathbf{C} \mathbf{c}_t + \mathbf{w}_t \\
\mathbf{y}_t = \mathbf{Z} \mathbf{x}_t + \mathbf{a} + \mathbf{v}_t
$$
would give
\[ \mathbf{x}_t = \mathbf{B} \mathbf{x}_{t-1} + \mathbf{C} \mathbf{c}_t + \mathbf{w}_t \\ \mathbf{y}_t = \mathbf{Z} \mathbf{x}_t + \mathbf{a} + \mathbf{v}_t \]
You can also use some additional LaTeX options
inside the equation block for additional formatting options. For
example, the aligned command can be used with an ampersand
& to align multiple equations, such that
\begin{aligned}
y &= 2x + x^2 + 3 \\
&= x(2 + x) + 3
\end{aligned}
yields
\[ \begin{aligned} y &= 2x + x^2 + 3 \\ &= x(2 + x) + 3 \end{aligned} \]
It turns out that pandoc won’t properly render multiline equations in
.pdf format when demarking them with double dollar signs
($$). Instead, you’ll need to use the
LaTeX commands \begin{equation} and
\end{equation} to set them apart. For example,
\begin{equation}
y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\
e_{i,j} \sim \text{N}(0, \sigma^2)
\begin{equation}
will render to
\[\begin{equation} y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\ e_{i,j} \sim \text{N}(0, \sigma^2) \end{equation}\]
It turns out that this format works with .html formats
as well, so you may just want to get in the habit of using this
form.
There are several ways to create tables in R
Markdown documents, but they vary in format based on your
chosen output format. For .html documents, you can create
simple tables with pipes (|) and colons (:).
For example,
| Tables | Are | Cool |
| ------------- |:-------------:| -----:|
| col 3 is | right-aligned | $1600 |
| col 2 is | centered | $12 |
| col 1 is | left-aligned | $1 |
will result in
| Tables | Are | Cool |
|---|---|---|
| col 3 is | right-aligned | $1600 |
| col 2 is | centered | $12 |
| col 1 is | left-aligned | $1 |
Note that the above code has been formatted for easier reading, but you wouldn’t have to do that. For example,
| Tables | Are | Cool |
| --- |:---:| ---:|
| col 3 is | right-aligned | $1600 |
| col 2 is | centered | $12 |
| col 1 is | left-aligned | $1 |
will give the same result
| Tables | Are | Cool |
|---|---|---|
| col 3 is | right-aligned | $1600 |
| col 2 is | centered | $12 |
| col 1 is | left-aligned | $1 |
{kableExtra}You can create much fancier tables with the {kableExtra}
package (click here
for the vignette with lots of examples). For example, the following code
will create a table with striped rows, custom column widths, and a
scroll box.
## load package
library(kableExtra)
## create exanple data frame
tbl_txt <- palmerpenguins::penguins[1:20, c(1, 2, 8, 7, 6)]
colnames(tbl_txt) <- c("Species", "Island", "Year", "Sex", "Body mass")
## generate table
kable(tbl_txt, format = "html",
caption = "Table 1. An example of a `kableExtra` table.",
align = "ccccr", escape = FALSE) %>%
kable_styling(bootstrap_options = "striped",
full_width = FALSE,
position = "left") %>%
column_spec(c(1,3,4,5), width = "6em") %>%
column_spec(2, width = "12em") %>%
scroll_box(height = "300px", extra_css = "border-style: none;")
| Species | Island | Year | Sex | Body mass |
|---|---|---|---|---|
| Adelie | Torgersen | 2007 | male | 3750 |
| Adelie | Torgersen | 2007 | female | 3800 |
| Adelie | Torgersen | 2007 | female | 3250 |
| Adelie | Torgersen | 2007 | NA | NA |
| Adelie | Torgersen | 2007 | female | 3450 |
| Adelie | Torgersen | 2007 | male | 3650 |
| Adelie | Torgersen | 2007 | female | 3625 |
| Adelie | Torgersen | 2007 | male | 4675 |
| Adelie | Torgersen | 2007 | NA | 3475 |
| Adelie | Torgersen | 2007 | NA | 4250 |
| Adelie | Torgersen | 2007 | NA | 3300 |
| Adelie | Torgersen | 2007 | NA | 3700 |
| Adelie | Torgersen | 2007 | female | 3200 |
| Adelie | Torgersen | 2007 | male | 3800 |
| Adelie | Torgersen | 2007 | male | 4400 |
| Adelie | Torgersen | 2007 | female | 3700 |
| Adelie | Torgersen | 2007 | female | 3450 |
| Adelie | Torgersen | 2007 | male | 4500 |
| Adelie | Torgersen | 2007 | female | 3325 |
| Adelie | Torgersen | 2007 | male | 4200 |
Another of Markdown’s strengths is its ability to render high-quality figures. This can be done by either inserting links to saved figures/images as shown above, or executing R code to do so. For example, this code
```{r xy_plot}
set.seeed(123)
n <- 100
x <- runif(nn, 0, 10)
e <- rnorm(nn)
y <- 1 + 0.5 * x + e
plot(x, y)
```
would produce the following plot
You can also add chunk options to change the figure’s size, location, etc. For example,
```{r xy_plot, fig.height = 4, fig.width = 4, fig.align = "center"}
set.seed(497)
n <- 100
x <- runif(n, 0, 10)
e <- rnorm(n)
y <- 1 + 0.5 * x + e
plot(x, y)
```
would instead yield
R Markdown is set up to use
BibTeX-style references and format the citations
accordingly. To do so, you’ll need to have your references in a
BibTeX library with a .bib extension.
.bib fileOne option is to manually create reference entries, but there are several methods for exporting references from reference management software, such as EndNote or Zotero.
To export your citations from Zotero, do the following
File > Export LibraryBibTeX from the dropdown
menu & click OK.bib suffixTo export a reference library from EndNote, do the following
Edit > Output Styles > Open Style Manager...Enter “bibtex” into the search bar at the top of the pop-up
window and check the box next to BibTeX Export
Close the window when you’re finished
Edit > Output Styles and
check the BibTeX Export optionFrom the main menu, select
File > Export...
Make sure to give your filename a .bib suffix and
verify that the options Text only and
BibTeX Export are selected
Click Save when you’re finished
To export a reference library from Mendeley, do the following
Go to the Mendeley Preferences menu
Click on the BibTeX tab
Check the box next to Enable BibTeX syncing
Click the radio button next to
Create one BibTeX file per group
Change the Path to your desired location for the
library files
Click OK when you are finished
The first step in getting properly formatted citations and references in R Markdown documents is to specify two pieces of information in the documents YAML:
the name of of the .bib file containing the
references
the name of the style file that specifies how the references will be formatted in the printed docuement.
So, for example, the information for this document is
bibliography: "references.bib"
csl: "ecology.csl"
You can download just about any journal’s style file here.
There are two options for citations in R Markdown
documents, both based upon the standard Author Year format.
BibTeX entries have a “citekey” that begins with
@ by which they can be referenced. So, for example, if we
had this reference in our .bib library
@Article{Smith_2021,
year = {2021},
publisher = {The Ecological Society of America},
volume = {123},
number = {2},
pages = {1-10},
author = {Sarah Smith and Joe Johnson},
title = {Probably the best paper ever written},
journal = {Ecology},
}
we could use [@Smith_2021] to format the in-text
reference as “(Smith and Johnson 2021)”, or we could use
@Smith_2021 to format the in-text reference as “Smith and
Johnson (2021)”.
{knitcitations} packageCarl Boettiger and
colleagues have created a really neat package called
knitcitations for creating and citing
BibTeX-style references via several mechanisms. To
begin, you load the package and then use the cleanbib()
function to remove any old .bib files.
## load the package
library("knitcitations")
## clean out any existing .bib files
cleanbib()
## set pandoc for formatting
options("citation_format" = "pandoc")
You can cite an article by its DOI, using either citep()
or citet(), and the full citation information will be
gathered automatically. For example, the inline command
`r citep("10.1890/11-0011.1")`
will do two things:
create an (Author[s] Year) inline citation that
looks like (Abrams et al.
2012)
create the following BibTeX reference that can
be cited elsewhere using [@Abrams_2012] or
@Abrams_2012:
@Article{Abrams_2012,
doi = {10.1890/11-0011.1},
url = {https://doi.org/10.1890/11-0011.1},
year = {2012},
month = {feb},
publisher = {Wiley},
volume = {93},
number = {2},
pages = {281--293},
author = {Peter A. Abrams and Lasse Ruokolainen and Brian J. Shuter and Kevin S. McCann},
title = {Harvesting creates ecological traps: consequences of invisible mortality risks in predator{\textendash}prey metacommunities},
journal = {Ecology},
}
On the other hand, the inline command
`r citet("10.1098/rspb.2013.1372")`
will do two things:
create an Author[s] (Year) inline citation that
looks like Boettiger and Hastings
(2013)
create the following BibTeX reference that can
be cited elsewhere using [@Boettiger_2013] or
@Boettiger_2013:
@Article{Boettiger_2013,
doi = {10.1098/rspb.2013.1372},
url = {https://doi.org/10.1098/rspb.2013.1372},
year = {2013},
month = {sep},
publisher = {The Royal Society},
volume = {280},
number = {1766},
pages = {20131372},
author = {Carl Boettiger and Alan Hastings},
title = {No early warning signals for stochastic transitions: insights from large deviation theory},
journal = {Proceedings of the Royal Society B: Biological Sciences},
}
We can also cite BibTeX objects directly, such as
those that R provides for citing packages using the
citation() function. So, for example, here are the
citations for the {knitr} package
citation("knitr")
##
## To cite the 'knitr' package in publications use:
##
## Yihui Xie (2023). knitr: A General-Purpose Package for Dynamic Report
## Generation in R. R package version 1.42.
##
## Yihui Xie (2015) Dynamic Documents with R and knitr. 2nd edition.
## Chapman and Hall/CRC. ISBN 978-1498716963
##
## Yihui Xie (2014) knitr: A Comprehensive Tool for Reproducible
## Research in R. In Victoria Stodden, Friedrich Leisch and Roger D.
## Peng, editors, Implementing Reproducible Computational Research.
## Chapman and Hall/CRC. ISBN 978-1466561595
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
We can use the following inline command
`r citep(citation("knitr"))`
to generate the 3 BibTeX objects as
@InCollection{Xie_2014,
booktitle = {Implementing Reproducible Computational Research},
editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
year = {2014},
note = {ISBN 978-1466561595},
url = {http://www.crcpress.com/product/isbn/9781466561595},
}
@Book{Xie_2015,
title = {Dynamic Documents with {R} and knitr},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2015},
edition = {2nd},
note = {ISBN 978-1498716963},
url = {https://yihui.org/knitr/},
}
@Manual{Xie_2020,
title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
author = {Yihui Xie},
year = {2020},
note = {R package version 1.30},
url = {https://yihui.org/knitr/},
}
and also create the citation
(Xie 2014, 2015, 2023)
We can now cite the package with normal BibTeX entries and pandoc will correctly avoid duplicating the author’s name. For example,
[@Xie_2014; @Xie_2015; @Xie_2020]
will produce
(Xie 2014, 2015, Xie_2020?)
Similarly, we can cite references that are already included in our
.bib file using the standard notation, such that
[@Boettiger_2013] or @Boettiger_2013
will render as
(Boettiger and Hastings 2013) or Boettiger and Hastings (2013)
When citep() or citet() are called, they
automatically generate a BibTeX key in the format
AuthorLastName_Year. We can then use this key to cite a
reference without remembering its DOI. For example,
`r citep("Abrams_2012")`
will simply create the citation
(Abrams et al. 2012)
Creating the final references cited section is straightforward. All
we have to do is call the function write.bibtex() with the
name of the .bib file and the references will be cited with
the formatting specified in the .cls file supplied in the
document’s YAML. For example, we can generate the references cited
section from the citations in this tutorial with the following:
## create ref cited section
write.bibtex(file = "references.bib")